Starting phenix.real_space_refine on Wed Jun 4 20:46:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnb_34909/06_2025/8hnb_34909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnb_34909/06_2025/8hnb_34909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnb_34909/06_2025/8hnb_34909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnb_34909/06_2025/8hnb_34909.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnb_34909/06_2025/8hnb_34909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnb_34909/06_2025/8hnb_34909.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 2689 2.51 5 N 649 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4083 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4041 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 3 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 189 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.51, per 1000 atoms: 2.08 Number of scatterers: 4083 At special positions: 0 Unit cell: (101.504, 59.072, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 713 8.00 N 649 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.04 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.04 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 531.9 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 69.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 26 through 60 removed outlier: 4.140A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 removed outlier: 3.900A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.794A pdb=" N LEU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.588A pdb=" N MET A 118 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.546A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.596A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.971A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.782A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.516A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.923A pdb=" N PHE A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.212A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 401 removed outlier: 3.846A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.571A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.131A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.515A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.710A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.597A pdb=" N LEU A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 4.442A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.594A pdb=" N PHE A 501 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER A 492 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 503 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 602 removed outlier: 7.059A pdb=" N THR A 615 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP A 602 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS A 613 " --> pdb=" O TRP A 602 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 744 1.33 - 1.45: 1084 1.45 - 1.57: 2302 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 4178 Sorted by residual: bond pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 1.409 1.481 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA ALA A 581 " pdb=" C ALA A 581 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.75e+00 bond pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 1.520 1.557 -0.037 1.26e-02 6.30e+03 8.62e+00 bond pdb=" C GLN A 369 " pdb=" N PRO A 370 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.23e+00 bond pdb=" C TYR A 640 " pdb=" O TYR A 640 " ideal model delta sigma weight residual 1.236 1.205 0.032 1.15e-02 7.56e+03 7.57e+00 ... (remaining 4173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 5330 2.65 - 5.30: 293 5.30 - 7.94: 45 7.94 - 10.59: 6 10.59 - 13.24: 2 Bond angle restraints: 5676 Sorted by residual: angle pdb=" N TYR A 121 " pdb=" CA TYR A 121 " pdb=" C TYR A 121 " ideal model delta sigma weight residual 109.15 98.24 10.91 1.44e+00 4.82e-01 5.74e+01 angle pdb=" N PHE A 591 " pdb=" CA PHE A 591 " pdb=" C PHE A 591 " ideal model delta sigma weight residual 111.14 104.03 7.11 1.08e+00 8.57e-01 4.33e+01 angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" C GLU A 364 " ideal model delta sigma weight residual 111.36 118.51 -7.15 1.09e+00 8.42e-01 4.30e+01 angle pdb=" N LEU A 113 " pdb=" CA LEU A 113 " pdb=" C LEU A 113 " ideal model delta sigma weight residual 109.81 123.05 -13.24 2.21e+00 2.05e-01 3.59e+01 angle pdb=" N TYR A 502 " pdb=" CA TYR A 502 " pdb=" C TYR A 502 " ideal model delta sigma weight residual 110.42 119.66 -9.24 1.55e+00 4.16e-01 3.55e+01 ... (remaining 5671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 2303 21.06 - 42.12: 133 42.12 - 63.18: 16 63.18 - 84.24: 2 84.24 - 105.30: 8 Dihedral angle restraints: 2462 sinusoidal: 861 harmonic: 1601 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -129.16 43.16 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual 123.40 135.31 -11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" C ILE A 407 " pdb=" N ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 2459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 523 0.083 - 0.166: 114 0.166 - 0.249: 23 0.249 - 0.332: 8 0.332 - 0.415: 5 Chirality restraints: 673 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA SER A 140 " pdb=" N SER A 140 " pdb=" C SER A 140 " pdb=" CB SER A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 670 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.290 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG A 701 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.140 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG B 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1748 2.89 - 3.39: 4409 3.39 - 3.89: 6500 3.89 - 4.40: 7456 4.40 - 4.90: 12134 Nonbonded interactions: 32247 Sorted by model distance: nonbonded pdb=" O SER A 140 " pdb=" N CYS A 485 " model vdw 2.382 3.120 nonbonded pdb=" O3 NAG B 1 " pdb=" O5 NAG B 2 " model vdw 2.455 3.040 nonbonded pdb=" OG SER A 328 " pdb=" CD2 LEU A 570 " model vdw 2.458 3.460 nonbonded pdb=" N GLY A 223 " pdb=" N PHE A 224 " model vdw 2.460 2.560 nonbonded pdb=" N SER A 457 " pdb=" O SER A 457 " model vdw 2.496 2.496 ... (remaining 32242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 29.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.209 4188 Z= 0.513 Angle : 1.390 13.985 5699 Z= 0.925 Chirality : 0.083 0.415 673 Planarity : 0.016 0.261 698 Dihedral : 14.650 105.302 1421 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.09 % Allowed : 9.92 % Favored : 87.99 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.33), residues: 554 helix: 0.20 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 259 HIS 0.003 0.001 HIS A 575 PHE 0.014 0.001 PHE A 574 TYR 0.025 0.002 TYR A 338 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.15224 ( 2) link_NAG-ASN : angle 8.27917 ( 6) link_BETA1-4 : bond 0.04861 ( 1) link_BETA1-4 : angle 9.14291 ( 3) hydrogen bonds : bond 0.22210 ( 259) hydrogen bonds : angle 8.19178 ( 768) SS BOND : bond 0.00758 ( 7) SS BOND : angle 1.49258 ( 14) covalent geometry : bond 0.00702 ( 4178) covalent geometry : angle 1.34865 ( 5676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.404 Fit side-chains REVERT: A 48 MET cc_start: 0.8622 (tpt) cc_final: 0.8343 (tpt) REVERT: A 115 HIS cc_start: 0.7412 (t-90) cc_final: 0.7135 (t-90) REVERT: A 332 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6262 (mm) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 0.1822 time to fit residues: 27.6267 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.236262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.182763 restraints weight = 4433.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.187110 restraints weight = 2588.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189420 restraints weight = 1882.286| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4188 Z= 0.178 Angle : 0.771 12.857 5699 Z= 0.365 Chirality : 0.044 0.326 673 Planarity : 0.004 0.030 698 Dihedral : 7.650 59.628 656 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 16.97 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.33), residues: 554 helix: 1.23 (0.27), residues: 332 sheet: -5.43 (0.47), residues: 5 loop : -1.18 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.016 0.001 PHE A 73 TYR 0.019 0.002 TYR A 338 ARG 0.008 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01585 ( 2) link_NAG-ASN : angle 6.21248 ( 6) link_BETA1-4 : bond 0.01493 ( 1) link_BETA1-4 : angle 2.28973 ( 3) hydrogen bonds : bond 0.05717 ( 259) hydrogen bonds : angle 5.11687 ( 768) SS BOND : bond 0.00214 ( 7) SS BOND : angle 0.84584 ( 14) covalent geometry : bond 0.00378 ( 4178) covalent geometry : angle 0.74245 ( 5676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.1952 time to fit residues: 25.7666 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.225437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.170752 restraints weight = 4567.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.175382 restraints weight = 2616.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178147 restraints weight = 1878.921| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4188 Z= 0.165 Angle : 0.718 12.341 5699 Z= 0.343 Chirality : 0.042 0.287 673 Planarity : 0.004 0.035 698 Dihedral : 5.766 59.514 654 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.96 % Allowed : 19.06 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.35), residues: 554 helix: 1.39 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 602 HIS 0.015 0.003 HIS A 115 PHE 0.012 0.001 PHE A 73 TYR 0.040 0.002 TYR A 590 ARG 0.007 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01534 ( 2) link_NAG-ASN : angle 5.96954 ( 6) link_BETA1-4 : bond 0.00604 ( 1) link_BETA1-4 : angle 0.82845 ( 3) hydrogen bonds : bond 0.05144 ( 259) hydrogen bonds : angle 4.73988 ( 768) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.77273 ( 14) covalent geometry : bond 0.00370 ( 4178) covalent geometry : angle 0.69179 ( 5676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.476 Fit side-chains REVERT: A 48 MET cc_start: 0.8863 (tpt) cc_final: 0.8595 (tpt) REVERT: A 93 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7718 (mtm180) REVERT: A 176 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7303 (tpp) REVERT: A 580 ARG cc_start: 0.7190 (ttp-110) cc_final: 0.6855 (ttm-80) outliers start: 19 outliers final: 9 residues processed: 103 average time/residue: 0.2429 time to fit residues: 30.6398 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 0.0060 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 27 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.194229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134954 restraints weight = 4776.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140810 restraints weight = 2317.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144547 restraints weight = 1483.980| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4188 Z= 0.131 Angle : 0.678 12.254 5699 Z= 0.320 Chirality : 0.041 0.264 673 Planarity : 0.004 0.035 698 Dihedral : 5.434 53.580 654 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.39 % Allowed : 20.10 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.35), residues: 554 helix: 1.68 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 602 HIS 0.006 0.002 HIS A 115 PHE 0.013 0.001 PHE A 73 TYR 0.043 0.002 TYR A 590 ARG 0.009 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01321 ( 2) link_NAG-ASN : angle 6.00484 ( 6) link_BETA1-4 : bond 0.00386 ( 1) link_BETA1-4 : angle 0.93687 ( 3) hydrogen bonds : bond 0.04532 ( 259) hydrogen bonds : angle 4.46398 ( 768) SS BOND : bond 0.00160 ( 7) SS BOND : angle 0.85123 ( 14) covalent geometry : bond 0.00279 ( 4178) covalent geometry : angle 0.64899 ( 5676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.421 Fit side-chains REVERT: A 27 LEU cc_start: 0.6426 (tt) cc_final: 0.5931 (tt) REVERT: A 117 PHE cc_start: 0.8301 (m-10) cc_final: 0.7953 (m-10) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1853 time to fit residues: 21.9059 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.187502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127928 restraints weight = 4987.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133504 restraints weight = 2425.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137118 restraints weight = 1572.720| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4188 Z= 0.173 Angle : 0.713 12.261 5699 Z= 0.335 Chirality : 0.041 0.256 673 Planarity : 0.004 0.043 698 Dihedral : 5.321 53.488 654 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.44 % Allowed : 20.37 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.35), residues: 554 helix: 1.55 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 204 PHE 0.013 0.001 PHE A 73 TYR 0.038 0.002 TYR A 590 ARG 0.009 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01262 ( 2) link_NAG-ASN : angle 6.01851 ( 6) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 0.97578 ( 3) hydrogen bonds : bond 0.04677 ( 259) hydrogen bonds : angle 4.43300 ( 768) SS BOND : bond 0.00098 ( 7) SS BOND : angle 0.79823 ( 14) covalent geometry : bond 0.00405 ( 4178) covalent geometry : angle 0.68602 ( 5676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.459 Fit side-chains REVERT: A 614 ARG cc_start: 0.8146 (mmt-90) cc_final: 0.7914 (mmp80) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.2209 time to fit residues: 26.2749 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.185355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125999 restraints weight = 4916.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131274 restraints weight = 2476.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134701 restraints weight = 1646.289| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4188 Z= 0.192 Angle : 0.725 12.300 5699 Z= 0.341 Chirality : 0.042 0.257 673 Planarity : 0.004 0.045 698 Dihedral : 5.294 53.118 654 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.92 % Allowed : 21.41 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 554 helix: 1.37 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.023 0.001 PHE A 117 TYR 0.036 0.002 TYR A 590 ARG 0.011 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01255 ( 2) link_NAG-ASN : angle 6.03318 ( 6) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 1.00446 ( 3) hydrogen bonds : bond 0.04709 ( 259) hydrogen bonds : angle 4.45996 ( 768) SS BOND : bond 0.00142 ( 7) SS BOND : angle 0.66745 ( 14) covalent geometry : bond 0.00467 ( 4178) covalent geometry : angle 0.69872 ( 5676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.470 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 0.2685 time to fit residues: 29.9334 Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 40.0000 chunk 48 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.186512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127691 restraints weight = 4873.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133147 restraints weight = 2355.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136672 restraints weight = 1527.161| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4188 Z= 0.156 Angle : 0.721 12.290 5699 Z= 0.336 Chirality : 0.041 0.252 673 Planarity : 0.004 0.052 698 Dihedral : 5.315 53.248 654 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.18 % Allowed : 21.15 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.35), residues: 554 helix: 1.46 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.006 0.002 HIS A 115 PHE 0.027 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.012 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01261 ( 2) link_NAG-ASN : angle 6.03504 ( 6) link_BETA1-4 : bond 0.00386 ( 1) link_BETA1-4 : angle 0.97073 ( 3) hydrogen bonds : bond 0.04471 ( 259) hydrogen bonds : angle 4.35478 ( 768) SS BOND : bond 0.00111 ( 7) SS BOND : angle 0.62792 ( 14) covalent geometry : bond 0.00371 ( 4178) covalent geometry : angle 0.69418 ( 5676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.406 Fit side-chains REVERT: A 29 MET cc_start: 0.8442 (mmt) cc_final: 0.8151 (mmt) REVERT: A 197 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: A 614 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.7975 (mtp85) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1997 time to fit residues: 22.3913 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127353 restraints weight = 4787.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132819 restraints weight = 2336.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136312 restraints weight = 1528.211| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4188 Z= 0.151 Angle : 0.710 12.285 5699 Z= 0.329 Chirality : 0.041 0.252 673 Planarity : 0.004 0.054 698 Dihedral : 5.275 53.425 654 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.66 % Allowed : 21.93 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.35), residues: 554 helix: 1.54 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -0.51 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.029 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.011 0.001 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01259 ( 2) link_NAG-ASN : angle 6.04006 ( 6) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 0.93367 ( 3) hydrogen bonds : bond 0.04351 ( 259) hydrogen bonds : angle 4.28769 ( 768) SS BOND : bond 0.00105 ( 7) SS BOND : angle 0.55912 ( 14) covalent geometry : bond 0.00351 ( 4178) covalent geometry : angle 0.68337 ( 5676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.423 Fit side-chains REVERT: A 176 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7246 (mmm) REVERT: A 197 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: A 614 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.8008 (mtp85) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.2047 time to fit residues: 23.5334 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.0670 chunk 24 optimal weight: 0.4980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.187934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128892 restraints weight = 4800.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134358 restraints weight = 2357.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138080 restraints weight = 1538.552| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4188 Z= 0.146 Angle : 0.712 12.286 5699 Z= 0.329 Chirality : 0.041 0.250 673 Planarity : 0.004 0.057 698 Dihedral : 5.280 53.392 654 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.66 % Allowed : 21.41 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.36), residues: 554 helix: 1.59 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.37 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.006 0.002 HIS A 115 PHE 0.028 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.014 0.002 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01269 ( 2) link_NAG-ASN : angle 6.04079 ( 6) link_BETA1-4 : bond 0.00427 ( 1) link_BETA1-4 : angle 0.95902 ( 3) hydrogen bonds : bond 0.04274 ( 259) hydrogen bonds : angle 4.25894 ( 768) SS BOND : bond 0.00088 ( 7) SS BOND : angle 0.53225 ( 14) covalent geometry : bond 0.00339 ( 4178) covalent geometry : angle 0.68543 ( 5676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.499 Fit side-chains REVERT: A 176 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7125 (mmm) REVERT: A 197 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 614 ARG cc_start: 0.8247 (mmt-90) cc_final: 0.8021 (mtp85) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.2700 time to fit residues: 31.1581 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 0.0870 chunk 31 optimal weight: 0.0570 chunk 11 optimal weight: 50.0000 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 0.0370 chunk 19 optimal weight: 30.0000 chunk 32 optimal weight: 0.5980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.191181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132516 restraints weight = 4835.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138192 restraints weight = 2348.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141873 restraints weight = 1514.040| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4188 Z= 0.134 Angle : 0.753 12.244 5699 Z= 0.342 Chirality : 0.041 0.247 673 Planarity : 0.004 0.059 698 Dihedral : 5.327 53.545 654 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.87 % Allowed : 23.24 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.36), residues: 554 helix: 1.71 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -0.41 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 171 HIS 0.004 0.001 HIS A 115 PHE 0.027 0.001 PHE A 117 TYR 0.036 0.001 TYR A 590 ARG 0.014 0.002 ARG A 532 Details of bonding type rmsd link_NAG-ASN : bond 0.01266 ( 2) link_NAG-ASN : angle 6.04260 ( 6) link_BETA1-4 : bond 0.00407 ( 1) link_BETA1-4 : angle 0.94842 ( 3) hydrogen bonds : bond 0.04074 ( 259) hydrogen bonds : angle 4.12838 ( 768) SS BOND : bond 0.00059 ( 7) SS BOND : angle 0.43150 ( 14) covalent geometry : bond 0.00300 ( 4178) covalent geometry : angle 0.72831 ( 5676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.522 Fit side-chains REVERT: A 56 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7639 (tp30) REVERT: A 170 MET cc_start: 0.8450 (mmm) cc_final: 0.8194 (mmp) REVERT: A 197 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: A 246 ARG cc_start: 0.8979 (mmp80) cc_final: 0.8757 (mmp80) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.2796 time to fit residues: 32.7994 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 0.0050 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.187881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129723 restraints weight = 4860.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135054 restraints weight = 2433.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138491 restraints weight = 1589.754| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4188 Z= 0.155 Angle : 0.775 13.616 5699 Z= 0.349 Chirality : 0.043 0.251 673 Planarity : 0.004 0.036 698 Dihedral : 5.289 53.504 654 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 24.80 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.36), residues: 554 helix: 1.67 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.33 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.006 0.001 HIS A 115 PHE 0.024 0.001 PHE A 391 TYR 0.035 0.002 TYR A 590 ARG 0.007 0.001 ARG A 580 Details of bonding type rmsd link_NAG-ASN : bond 0.01263 ( 2) link_NAG-ASN : angle 6.03585 ( 6) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 0.92223 ( 3) hydrogen bonds : bond 0.04300 ( 259) hydrogen bonds : angle 4.18819 ( 768) SS BOND : bond 0.00066 ( 7) SS BOND : angle 0.50573 ( 14) covalent geometry : bond 0.00368 ( 4178) covalent geometry : angle 0.75071 ( 5676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.06 seconds wall clock time: 47 minutes 3.13 seconds (2823.13 seconds total)